GENCODE reference annotation for the human and mouse genomes

A Frankish, M Diekhans, AM Ferreira… - Nucleic acids …, 2019 - academic.oup.com
The accurate identification and description of the genes in the human and mouse genomes
is a fundamental requirement for high quality analysis of data informing both genome …

GENCODE: the reference human genome annotation for The ENCODE Project

J Harrow, A Frankish, JM Gonzalez, E Tapanari… - Genome …, 2012 - genome.cshlp.org
The GENCODE Consortium aims to identify all gene features in the human genome using a
combination of computational analysis, manual annotation, and experimental validation …

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

S Pujar, NA O'Leary, CM Farrell… - Nucleic Acids …, 2018 - academic.oup.com
Abstract The Consensus Coding Sequence (CCDS) project provides a dataset of protein-
coding regions that are identically annotated on the human and mouse reference genome …

GENCODE: reference annotation for the human and mouse genomes in 2023

A Frankish, S Carbonell-Sala, M Diekhans… - Nucleic acids …, 2023 - academic.oup.com
GENCODE produces high quality gene and transcript annotation for the human and mouse
genomes. All GENCODE annotation is supported by experimental data and serves as a …

GENCODE: producing a reference annotation for ENCODE

J Harrow, F Denoeud, A Frankish, A Reymond… - Genome biology, 2006 - Springer
Background The GENCODE consortium was formed to identify and map all protein-coding
genes within the ENCODE regions. This was achieved by a combination of initial manual …

The state of play in higher eukaryote gene annotation

JM Mudge, J Harrow - Nature Reviews Genetics, 2016 - nature.com
A genome sequence is worthless if it cannot be deciphered; therefore, efforts to describe—
or'annotate'—genes began as soon as DNA sequences became available. Whereas early …

Current status and new features of the Consensus Coding Sequence database

CM Farrell, NA O'Leary, RA Harte… - Nucleic acids …, 2014 - academic.oup.com
Abstract The Consensus Coding Sequence (CCDS) project (http://www. ncbi. nlm. nih.
gov/CCDS/) is a collaborative effort to maintain a dataset of protein-coding regions that are …

The Ensembl automatic gene annotation system

V Curwen, E Eyras, TD Andrews, L Clarke… - Genome …, 2004 - genome.cshlp.org
As more genomes are sequenced, there is an increasing need for automated first-pass
annotation which allows timely access to important genomic information. The Ensembl gene …

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

KD Pruitt, J Harrow, RA Harte, C Wallin… - Genome …, 2009 - genome.cshlp.org
Effective use of the human and mouse genomes requires reliable identification of genes and
their products. Although multiple public resources provide annotation, different methods are …

ORegAnno: an open-access community-driven resource for regulatory annotation

OL Griffith, SB Montgomery, B Bernier… - Nucleic acids …, 2007 - academic.oup.com
ORegAnno is an open-source, open-access database and literature curation system for
community-based annotation of experimentally identified DNA regulatory regions …